My PhD mentor, Professor John Carr and I were raring to go. It would be our first fieldwork experience since I began my PhD at the University of Cambridge in the Molecular Virology Lab. We were on a virus discovery mission and primarily looking to catch viruses transmitted by aphids. We already knew that aphids were responsible for spreading most plant viruses affecting crops, including beans. This mission was to investigate whether aphids flying around in fields carry and transmit multiple plant-infecting viruses. The thought that aphids could serve as ‘dirty hypodermic needles’ is a scary prospect for farmers and researchers. We were keen to know the diversity of aphid species in the field and the viruses they spread. At Heathrow airport John turned to me and said
Our hosts in Kenya were Dr Appolinaire Djikeng and Dr Jagger Harvey, scientists at the Biosciences Eastern and Central Africa Hub (BecA-ILRI) at the International Livestock Research Institute (ILRI). ILRI is located on a beautiful campus on the west side of Nairobi, with quiet surroundings; it is abuzz with science. It was an unusual ‘homecoming’ for me. I had worked at ILRI as a research assistant before joining Cambridge University. Perhaps due to the hierarchical nature of science, I had never envisioned returning there as a visiting scientist, at least not so soon. But here we were, and ILRI would not disappoint in its hospitality and scientific readiness.
Dr James Wainaina, then a research assistant working with Jagger on aflatoxins joined John and I for the fieldwork. Jagger and John had met at Cambridge while Jagger was a postdoctoral researcher prior to taking up a scientist position at BecA-ILRI. But it was James who had the hook-up and social capital we needed. Over time he had forged strong connections with Dr David Karanja- the Kenya Agricultural and Livestock Research Organization National Bean Program Coordinator, and a host of farmers who grew beans. We were on borrowed time, for James was about to leave for his PhD studies in Australia in the laboratory of Dr Laura Boykin. His research interest was whiteflies on bean, which created a perfect convergence of our scientific interests.
Our journey took us to Katumani and into David Karanja’s fields. We were two weeks early. There were hardly any aphids in the area. Usually, aphids accumulate on beans as they flower and pod. At times they can be found on younger plants, but this was not the case at Katumani. Curiously, whiteflies were all over the place, which was great for James’ work. With David’s blessings, we headed for Kaiti, in Makueni- a richly agricultural county in Eastern Kenya. Beans and cowpea (another legume, scientific name: Vigna unguiculata and locally called ‘kunde’) were plentiful. There were no aphids on the bean crop there either. Instead, in our wandering through cowpea plots we found plenty of another closely related species of aphid (the cowpea aphid)- which was not what we wanted, save for scientific curiosity. It was a tough initiation into fieldwork for John and I.
The following morning, we set out for highlands of Kiambu to the farm of a Mr Njiiri where his wife and children received us. It was a smallholder farm in the classic sense, optimized to produce as much crop variety as possible. Sweet potato, maize, kale, tree tomato, the occasional beehive thrived alongside bean plots. Importantly, aphids were all over the place. Though we were happy to find aphids, Njiiri’s wife was not pleased. From the level of aphid infestation it was apparent that she was not keen to spray to kill the aphids. Some of the plants showed signs of disease. It may have been that either the pesticides were inaccessible or undesirable environmentally. Notably, part of her farmland was leased to other farmers who also did not use pesticides and whose cultivated plots would continue to be a source of aphids and infection.
As we were about to leave, she asked us in the precise way that farmers always speak ‘Will I harvest anything on those bean plots or do I just uproot everything’.
It was a poignant moment. Our next words were chosen carefully. We could tell the crop was lost to both disease and aphid infestation but had to hedge our words and actions to blunt the sharp edge of our assessment. So we said ‘Look, we have trampled all over your shamba, mama. Surely, anything you would have harvested here is almost gone. We are more than happy to compensate you in cash for allowing us to work in your bean plots’. Her wide smile indicated to us that our opening gambit was accepted. She would salvage something after all, and maybe have another go next season. Over that week, we found similar success trapping aphids in smallholder farm in Oloirien and Oloolua in Kajiado. We also found despondency in farmers caused by insect and virus burdens- their efforts would not translate into bumper harvests.
Back at Beca-ILRI hub, we prepared the samples for High Throughput Sequencing on the Illumina Platform. Like all ‘clever-thinking’ scientists, we had a fair expectation of what we would get, but nature is full of surprises. The initial bioinformatics analyses were conducted by Joyce Njuguna, who is now a PhD student at the University of Illinois – Urbana Champagne. I was back in the UK when her call explaining the findings came though.
Dicistroviruses are remarkable insect-infecting viruses; they use plants as reservoirs to infect their insect hosts. They can in some cases kill aphids, decrease their reproduction, or cause confusion which predisposes aphids to attacks by predators and parasitoids. Concurrently, another researcher, Dr Luke Braidwood, detected similar and related viruses in maize while searching for components for maize lethal necrosis disease which at the time was wreaking havoc for maize farmers in East and Central Africa. This finding of dicistroviruses was the first report for these viruses in the black bean aphid globally.
My current research explores the use of these potentially beneficial distroviruses for crop protection (bio-control). Hopefully, we shall put a halt to aphid infestation and secure better yields for farmers by protecting crops without wrecking the environment.
Dr Wamonje is a FLAIR Research Fellow and Founder of The Centre for Plant Pathogen Interactions Research. We welcome comments, experiences and tips from all walks of life that can enrich this topic.